RNA interference (RNAi) is a mechanism endogenously existing in cells to suppress the expression of genes through interaction of protein complexes with the mRNA. Naturally occurring RNAi relies on microRNAs. MicroRNAs (miRNA) are processed from RNAs sequences that fold into an internal stem-loop structure. 5′ and 3′ adjacent sequences are cut off as well as the loop leaving a short double stranded RNA with usually 2 nucleotides overhangs on the 3′ end of each strand. One of the strands is degraded while the other strand remains (the guide strand). The guide strand is incorporated into a protein complex leading to degradation or translational repression of mRNA targets, which are at least partially complementary. The mechanism of RNAi has been artificially employed since several years now by the introduction of shRNA stem-loop sequences that are processed like miRNA but due to full complementarity with the target mRNA always leads to its degradation. And there are siRNAs that are used as triggers of RNAi, which are already fully processed miRNA but usually contain full complementary strands and show full complementarity with the target RNA the same as processed shRNAs.
RNAi based therapy is very appealing due to its target specificity at very low doses, which can avoid common drug intrinsic side effects. Furthermore, in case of long term treatment like gene therapy RNAs have the advantage to be not prone to immune response while proteins are.
However, current siRNAs and shRNAs (collectively, “si/shRNAs”) targeting mammalian genes or pathologic mRNAs (like viruses for example) are designed based on actual sequences occurring in nature. In case of viruses that mutate the design, it relies on the identification of conserved regions in naturally available strain sequences. But, even conserved regions are not without mutations and the therapeutic pressure of therapeutic si/shRNAs readily leads to escape variants which render these si/shRNAs ineffective. Prime examples to generate escape strains are Human Immunodeficiency virus (HIV), Hepatitis C virus (HCV) and Hepatitis B virus (HBV). Therefore, it would be desired to generate universal RNA interference molecules that would retain their efficacy when such viruses mutate.